Not Quiet Deletion
by Glorifield
Summary: What happens to programs one doesn't want but could be useful later? Based after the trilogy. Rated T just in case. Smith/Persephone... eventually.
1. Prologue

**Disclaimer- don't own the Matrix, never will**

**Prologue **

There was rain, there was Mr. Anderson, then there was pain- or as close to pain as he had ever experienced. He felt his code being ripped and scattered. _Deletion_, he thought, _I will be deleted and it will all be over._ The thought wasn't sad or angry, just a fact. He had always wanted to leave the Matrix, and now he was going to do so.

Then something changed. It was being brought together. Green lines of code formed, once again, a man. The rain had stopped but the chill remained. Whole now, Smith opened cold blue eyes only to wonder if he had opened them. Removing his shades and placing them neatly in his inner pocket, he realized it wasn't completely dark. A dark gray fog swirled around in what seemed to be an unlimited space. Above, below, and around him- he appeared to be standing in a storm cloud. _What trick is this? _"Mr. Anderson, I'm aware that your kind might find this amusing, but know that I will find you. It is inevitable."

He took a few quick, yet deliberate steps forward, only to knocked backwards. _A wall?_ There was nothing to indicate a barrier; not even the codes read as a wall of any sort. Smith adjusted the cuffs of his suit, calming himself before reaching out. _There!_ He followed it, hitting a corner at six and one half steps exactly. The same at the next wall and the next, until he reached his original point. _No NO NO!_ "NO!" He pounded the wall with all his strength. "Where IS THIS?!"


	2. Chapter 1

I don't own the Matrix. Also, as a disclaimer, this is the first fanfic I have ever put to paper/screen. I apologize for the lack of experience ^_^;

**Chapter 1**

**One year later-**

Morpheus stood upright, all surprise contained. "And the rouge agent, what of him?"

The couple in front of him were seated at an elegant dinner table.

The Merovingian turned up the corners of his mouth, "let us say, he is in ze recycle bin of sorts." He laughed in a humming sort of way and placed a plump grape in his mouth.

Morpheus turned his head slightly. Persephone, sensing his confusing, said, "He has been put aside. The machines have found him too dangerous to keep around, yet too useful to delete completely." She glanced at her husband and then continued sipping from a crystal wine glass.

"I don't fully understand."

"But ze concept is so simple," cooed the Merovingian, "If the matrix is a computer system zere would have to be a recycle bin. It's a smaller matrix within the matrix. Do you see?"

Persephone, again, noticed the confusion. "The former Agent Smith had many… human-like qualities that the machines want desperately to understand. He was the best of his kind for this reason. Even so, it lead him to confusing and rebellion."

The coded goddess flashed her large brown eyes at the rebel hero, "Please excuse me. I have to attend to something." She slid gracefully from her chair, never losing eye contact with Morpheus, then left the dining hall.

The Merovingian's smirk only widened. "Ah les femmes, so predictable, so easy to read. Cause and effect is the only rule one needs to follow." There was a pregnant pause. "You should know, I came across such a beautiful woman the other night. Aristocratic type, so… so … I believe the word is _refined_. …Yes, I know her games by now. We shall play them until the end of this magnificent world."

The French man did not protest when Morpheus followed Persephone's example out the door.

She was waiting for him. He knew she would be. "You must free him."

Morpheus regarded her quizzically. "I don't believe that would be wise."

She stepped forward so that she could almost disappear inside his jacket. "The machines, they plan to wipe his memory of everything before Neo then release him into Zion's mainframe. He'll do what all viruses do. You understand the danger of this, don't you?"

The man simply nodded.

"You'llhave to get to the recycle bin"

"And I suppose you know where it is?"

"Naturally"

Morpheus looked at her from over his shades. "What do you want?"

Persephone practically breathed her words, "you know what I charge." Her arms snaked under his jacket and around to his back, fingers dancing to his shoulder blades. He took a firm step backwards.

"I'll have to consult the Oracle."

He left Persephone pouting and her husband quaintly eating a dessert of crème brule.


	3. Chapter 2

**I do not own The Matrix. Also, I would like to thank Digital Angel and Yarkelf for such kind reviews. You both made my day :)**

**Chapter 2**

_Photochemical smog, perhaps? No, it's not real. But, in that case I'm not real? Where is he? __**He**__ put me here! To what purpose? It makes no sense! DAMN HIM! He could have killed me. My code was fading, gone. _"gone"

The former agent was crumpled in the corner of his prison, occasionally mumbling his thoughts aloud. In the recent months he hadn't moved except in fits of anger. Currently, he was trying to dig his nails into the non-existent floor with a twitch-like motion. "Why? Why? WHY?!" He snarled, now clawing at his own hair. "I _will _kill you, Mr. Anderson! This…" He stood up weakly and held his hands upward like a preacher, "this place, this prison will not hold me forever!"

Having spent his energy, Smith slumped back into his corner, letting his head hang limply towards his chest.

It was at this second another man materialized in the cell. He looked Indian in origin, darkened skin and hair. He carried with him a small, worn suitcase. At first he seemed as lost as his cellmate, glancing around, taking in the clouds, the other man on the floor that appeared suspended against nothing, and the overall chill. Yet, unlike Smith, he seemed content with his surroundings. After giving a satisfied nod, he looked down at his cell mate.

In accented words, he said amiably, "I apologize for my lack of manners. My name is Rama-Kandra." He extended a hand towards Smith. The hand dropped as Smith sneered at it. Rama-Kandra, not the least discouraged, sat down against the adjacent wall. "You must be the notorious Agent Smith."

"Are you here to release me?" Smith managed to croak.

The man's smile fell. "I'm afraid not"

"If you will leave me like every other inefficient program that comes through here. I have no use for you." He turned away.

"Don't you want company? A nice conversation? Everything needs companionship"

Smith allowed for an intimating pause, finally focusing his gaze on Rama-Kandra. "Not I, never I. I had my selves and now I have myself."

Rama-Kandra raised his eyebrows ever so slightly. "What reason would you have to leave, then?"

For once in his existence, Smith did not have an answer and he did not like it. He sprung out of his corner with newfound engery. Heat began to rise in him. Clenching his teeth, he reached into his inner pocket, grasping for a Desert Eagle that wasn't there. "Arrgh! Get out of my sight!"

Smith threw a punch at the Indian, which Rama-Kandra easily dodged. Rama-Kandra looked at him with pity. "You are such a confused program. I truly hope you can find a reason."

The veins in Smith's neck were bulging as he heaved strained breaths. _Purpose, purpose, purpose, purpose… _

"Hmmm… I believe my end is here; it's been a good existence. That was a rather short meeting. Perchance we shall meet again, Agent Smith. Until then, perhaps you should think over what you want to do when you are released." With those words the man's code disappeared bit by bit, leaving Smith alone again.

He slid back into his previous position. _Purpose? Purpose. What drives, what to pursue….. Mr. Anderson. _


	4. Chapter 3

The Oracle was expecting them, as always. She swung the rickety door wide, revealing fresh cookies to the serious looking Niobe and Morpheus. The scene had an amusing contrast to it, one that did not escape the Indian girl watching it from the kitchen table. She giggled a bit as she stirred the next batch of cookie dough.

"Well now, why don't you two come inside?" She smiled widely, placing the cookies on a table and exchanging them for an already smoldering cigarette. "So tell me, when is this baby due?"

Niobe gingerly placed a hand on her bulging stomach, finally letting a small smile escape, herself. "Three more months"

The Oracle met the pregnant woman's eyes through wisps of cigarette smoke. "She's gonna be beautiful"

Morpheus got to the point. "I assume you know why we're here"

She sighed and turned her head to face him. Her shoulders tense. "You wish this visit to be short. Fine." She suffocated her cigarette in the crystal bowl that balanced dangerously on the scuffed kitchen table. "This is not a question of 'if' for, regardless of what I tell you today, someone will find a way of rescuing that confused program. …Oh dear, you don't have to clean that up…"

At that moment Niobe's cookie crumbled on the passage from her hand to her mouth. Crumbs, large and small, sprinkled the kitchen floor. "I'm so sorry." Niobe tried to bend over her large stomach but a small, scruffy dog beat her to it. It scrambled excitedly to Niobe's feet and licked up the offending pieces of cookie.

The older woman smiled again. "I told you so"

Niobe looked inquisitively at the dog as he scampered out of the kitchen.

"Oh him?" The Oracle followed her gaze. "You honestly don't think the lost programs are only humanoid, do you?"

Even Morpheus looked surprised at this.

"Anyway, as I was saying, Agent Smith will, one way or another, get out of the recycle bin. Persephone will find another way. She has… alternative motives. The decision that matters is what you do with him once he has been freed."

Morpheus nodded solemnly. "You're not going to tell us anything more, are you?"

She smiled and nodded. "You should know by now, Morpheus…"

He finished her sentence, "the decision has to be my own."

"Bingo"

* * *

Persephone led the way, followed closely by a guilty looking Morpheus and a furious Niobe. Persephone's short yet rapid steps reverberated in the hallway. A monotony of doors surrounded the odd group. Each door was identical to its neighbor, making any topic ridiculous to bring up. Persephone stopped abruptly, making it so Morpheus boots squeaked as he tried to avoid crashing.

"Here it is," she said as she placed her hand on the door. Her long, elegant fingers spread across the woodwork and a small click sounded from the knob. "I can go no farther; the entrance would consume any program that is not suppose to be there. I shall wait for you here."

She swung open the door to reveal another hallway indistinguishable from their current one.

"How will we know which door to choose?" Morpheus asked as he stepped through.

"I promise, you will recognize it and it will open with a push" She then turned to Niobe, who was still fuming. "I hope you will find it within yourself to forgive me. His passion…" at this she closed her eyes briefly, "take care not to lose him again."

Niobe took a short breath and marched through the door, closing it with meaning. "Bitch"

The door went on and on. Each one had no mark or sign that it could contain a furious ex-agent or have anything of value behind it at all.

"Morpheus, what if we passed it?"

"She said we would know, so we would know."

Continuing down the hall Niobe spotted it first. Morpheus was only a second behind. The door was a bright green and appeared to be made of plastic. Three white arrows, all pointing in a triangular shape were imprinted on it's front.

"Ya think this is it?" Niobe asked in a icy tone.

"Yes, I believe so." Morpheus pretended to take her seriously.

Niobe rolled her eyes and reached for the door.

"Wait." Morpheus grabbed her wrist gently. "Before we do this, I want you to know that it meant nothing. It was simply payment."

Niobe smiled. "I know. I just wanted to hear you say it."

The door opened easily, as Persephone had said it would. Yet, she had not warned about the pitiable sight that met them. The former Agent, once pressed and professional, was best described as crumpled. His suit had multiple tears, his hair was disheveled, one leg was bend as if trying to sit cross-legged while the other was jutting out diagonally, and his shades hung limply from one ear. He sat in a corner, lips moving as if he was reciting a long forgotten poem. His body was that of one defeated- eyes lowered and shoulders lopsided- no sign of determination.

Morpheus stepped hesitantly towards him. Agent Smith, who had once been so dangerous to him, who had once tortured him, now was brought so low. He felt a ting of pity. Rubbing his thumb along his other fingers he called out. "Smith?"

Smith's head snapped up and his body went rigid. "YOU!" His hands frantically felt in a his jacket for his nonexistent Desert Eagle. This plan failing, he scrabbled to his feet and ran, to the best of his ability, towards Morpheus. He tried pathetically to strangle him. "Where is Mr. Anderson?!" Shouting hoarsely and allowing spittle to escape from his mouth he continued, "Where is he?! WHERE?!? Where is MR…"

He was cut short. All pity leaving him, Morpheus had hit Smith with the butt of his gun, knocking the raging program unconscious.


	5. Chapter 4

**I do not own the Matrix or any of its characters. Sorry for the delay, everyone. I've been rather busy. The next chapter will be the last- hope you're enjoying the ride :) Thank you all for the kind reviews!**

**Chapter 4**

Persephone was waiting for them, flanked by the twins. As Morpheus emerged with Smith slung across his shoulder, her lips curved triumphantly.

"Marvelous," she breathed, gliding towards them. Her eyes flickered to each inch of the AI program. "Yes, yes you have done it" She extended her arm and gracefully stroked the side of his cheek. His body gave a small twitch. She quickly pulled back her hand. Her gaze fell on Morpheus. "We shall take care of things from here."

It took only seconds for the two parties to realize what was going on. A rapid succession of shuffling and clicks followed, as guns were brought into view. The twins had both guns aimed at Morpheus, Morpheus had his aimed at Persephone, Persephone had hers aimed at Niobe. Niobe had first pointed her gun at one of the twins, but thought better of it and turned towards Persephone. She smirked. "Just in case."

Neither the twins nor Persephone flinched. She appeared rather confident and spoke slowly. "You may think, Morpheus, that because I am a program I know nothing of the workings of a human heart. You would be wrong. I _know _you will not shoot me, for my gun is aimed at your love." The last world flowed out of her mouth with such emphasis, with such a melody, that even the twins' eyes seem to soften.

Morpheus' teeth ground together. He looked to Niobe's stern face. If it had been her, and her alone, he may have been torn between his mission and his love for her. But, her life wasn't the only one at stake. His gaze lowered to her stomach. The future of the matrix was in the children born outside of it.

Still holding his gun steady in one hand, he allowed Smith's body to slide down his arm and to the floor. The program rolled once then settled on his face. Everyone tensed; Niobe held her breath.

"Now," Persephone smirked and motioned to the twins. "Wasn't that easy for everyone?"

The left twin flipped Smith over, lifting him up by his shoulders. The right twin grabbed his ankles and they set off down the hallway. Persephone didn't lower her gun until the twins had safely disappeared behind a door.

"Thank you for…"

Niobe cut her off, gritting her teeth, "just _leave_"

* * *

Smith stirred a bit. He turned to one side, then the other, then back to the original side. He felt the soft covers restricting his movement. _Covers? _He jolted, eyes shooting wide open. He blinked a few times at the light. _light? _He slowly got out of the bed, standing in the middle of a grand room. A crystal chandelier hung from the ceiling, several statues were looking upon Smith in a apathetic way, the bed he just left was carved from some dark wood _probably a code for oak,_ and the carpet was thick and soft. Whoever lived here has a great amount of influence.

The former agent started adjusting the cuffs of his suit when he paused. He looked closer at the material, letting his gaze follow up his arm and eventually to the rest of his outfit.

"Do you like it?" Persephone stepped out from the shadowed corner of the room. "I was going to give you something more…… up to date, but I figured you would be more comfortable in what you are use to. It's very durable fabric, I promise."

Smith braced himself, fists clenched. He started to move forward, thought a second, and held back. "Why did you bring me here?" he growled.

Persephone stepped forward with confident strides; her silk dress bunched and released above her hips. Her hand reached up, coming within inches of Smith's forehead. Smith snatched her wrist with one hand and brushed the stray hairs back into place with the other hand.

"I repeat, why did you bring me here?" This time his voice carried the control and lethargy his programming encouraged.

She looked up at him through her eyelashes. "I have a business proposition for you."


	6. Chapter 5 end

**Well, here is the last chapter. Thank you for sticking with me this long; I hope you enjoyed the ride. Please review! This was my first fan fiction and I know I will have some bugs to work out. For all of you who did review, thank you so much! Your kind words encouraged me to complete this story.**

**a/n I DO NOT own The Matrix or its characters. I also do not own ****Life and Fate ****which is quoted below. **

"An electronic machine can carry out mathematical calculations, remember historical facts, play chess and translate books... It is able to solve mathematical problems more quickly than man and its memory is faultless. Is there any limit to progress, to its ability to create machines in the image and likeness of man? It seems the answer is no.

It is not impossible to imagine the machine of future ages and millennia. It will be able to listen to music and appreciate art; it will even be able to compose melodies, paint pictures and write poems. Is there a limit to its perfect? Can it be compared to man? Will it surpass him?

Childhood memories… tears of happiness… the bitterness of parting… love of freedom… feelings of pity for a sick puppy… nervousness… a mother's tenderness… thoughts of death… sadness… friendship… love of the weak… sudden hope… a fortunate guess… melancholy… unreasoning joy… sudden embarrassment…

The machine will be able to recreate all of this! But the surface of the whole earth will be too small to accommodate this machine- this machine whose dimensions and weight will continually increase as it attempts to reproduce the peculiarities of mind and soul of an average, inconspicuous human being" (Vasily Grossman, Life and Fate).

**Chapter 5**

"Can you bring me Mr. Anderson?"

Smith's eyebrows rose above his new shades. They stood there in silence, staring. A bystander would have thought them a couple about to dance. Finally, Persephone's gaze broke away.

"First, let me satisfy my curiosity" Her words were like honey flowing from her lips, yet the other program was unaffected by such things. She seemed fascinated with his tie for a bit and then her eyes snapped back to his face. She gently pulled her wrist from his grasp.

He watched her in casual fascination. He didn't even resist when she slid her hands into his, pulling them down by his side. He saw as her face drew closer to his own, yet waited to see what would happen. His eyes widened, hidden by his sunglasses, as her lips pushed against his.

Persephone knew what she was doing. She was gentle, yet passionate. Her lips and tongue worked on Smith's own lips and mouth like an artist's paintbrush on a canvas. A small gasp escaped from Smith, and Persephone released him, satisfied.

Smith's eyebrows knotted and his mouth came to resemble a sideways 's'. What were these sensations he felt? Not only in his lips but… Persephone began to talk, but he cut her off. Smith grabbed her head and pressed it towards his, almost smashing them together. His kisses were aggressive and lacked the finesse of Persephone's . Persephone didn't mind; she led by example, softening her kisses in return and stroking her hands down his neck and back. After several minutes of this, she nudged him back.

Fixing her hair so that it sank behind her shoulders, she began, "Now you must listen, you…"

"I demand to know what that was." Smith interrupted her.

"It was a deep symbol used by humans. Coded for pleasure and affection. A kiss," She seemed very pleased with his response. "You enjoyed it, didn't you?"

Smith's eyebrows knitted. His mouth, so active just a second ago, became set in a straight line.

"We," Persephone delicately traced the line of Smith's jaw and then placed her fingertips carefully above her chest, "we are capable of so much more than the average program. We were given something higher. Emotion makes us strong; obsessions make us powerful."

Smith remained silent, contemplative.

"You have mastered rage and greed already, my dear. And I have found desire and love. Perhaps if we could… expand our horizons, we could rule the Matrix. Think of it, you and I in control of both human and program. Why stop there? Zion is within our grasp. Understanding the human mind will make it so much easier to break into the mainframe. It's ours, ours for the taking!" She stepped closer to him, her eyes sparkling with excitement.

The former agent had one question. "What of Mr. Anderson? Surely he will stand in our way."

"The One is dead. The machines confirmed it."

Smith was a statue. Then he tilted his head. He actually _tilted his head_ like a child trying to figure something out. He grabbed Persephone's shoulders and gave her a hard, passionate kiss, taking deep breaths afterwards. He traced her waist and hip with his hand, whispering, "I will need a gun."

Persephone held her head high, a triumphant smile decorated her features. "Of course." She walked in a feline manner towards a dresser. Opening a small drawer she revealed a beautiful Desert Eagle. Smith held it in his hand for several seconds, just staring and then neatly placed it in his inner jacket pocket.

By the time Smith looked up, Persephone was already sitting on the corner of the bed. Smith attempted a lustful smile as he pushed her onto the comforter. He sat straddled on her body and in one fluid motion pulled the gun out of his jacket and aimed it downward.

BANG!

The goddess of the Matrix was sprawled artistically on the bed. She was bleeding beautifully from her stomach and her full lips parted for shallow breaths. All flashy code, really. Her program was simply disappearing line by line, but the Architect had a sense of the dramatic when it came to death.

Smith now stood at the foot of the bed, looking down at her. "Although you have give an interesting proposition, Ms. Persephone, I much prefer the simplicity of a program. We have a purpose and we follow it through, regardless of…" he spat out the next word, "_emotion._ Humans are too complicated, too messy. It makes them weak! Weak like Mr. Anderson was and weak like you apparently are. _Disgusting! _My old purpose is gone, but I must thank you for giving me a new one. Zion will be mine, and soon all will be mine. There is no One to stop me now, and I certainly do not need an accomplice. Your end was inevitable."

Persephone lay there, dead. She had probably died half way through his speech, but it couldn't be helped.

Smith turned and walked away from the bed. Pausing for a second at the doorway, he brushed his pointer finger across his lips and sighed. Firmly shaking his head he proceeded to step out into the world that would soon belong to him.


End file.
